dna/chem3/README.md

0001 \page ExampleChem3 Example chem3
0002
0003 ## General description
0004
0005 This example is provided by the Geant4-DNA collaboration.
0006
0007   These processes and models are further described at:
0008   http://geant4-dna.org
0009
0010   Any report or published results obtained using the Geant4-DNA software shall
0011   cite the following Geant4-DNA collaboration publications:
0012   Phys. Med. 31 (2015) 861-874
0013   Med. Phys. 37 (2010) 4692-4708
0014
0015   How to activate chemistry code.
0016   How to set minimum time step limits using TimeStepAction.
0017
0018 ## GEOMETRY DEFINITION
0019
0020   It is a simple sphere which represents a 'semi infinite' homogeneous medium.
0021
0022   Two parameters define the geometry :
0023    - the material of the sphere,
0024    - the full size of the sphere.
0025
0026   The default geometry is constructed in DetectorConstruction class, but all of
0027   the above parameters can be changed interactively via the commands defined in
0028   the DetectorMessenger class.
0029
0030 ## PHYSICS LIST
0031
0032   The physics list is initialized in G4EmDNAChemistry, together with chemical
0033   stage models configuration.
0034
0035 ## AN EVENT: THE PRIMARY GENERATOR
0036
0037   The primary kinematic consists of a single particle starting at the center of
0038   the sphere. The type of the particle and its energy are set in the
0039   PrimaryGeneratorAction class, and can be changed via the G4 build-in commands
0040   of G4ParticleGun class.
0041   The chemistry module is triggered in the StackingAction class when all
0042   physical tracks have been processed.
0043
0044 ## HOW TO START ?
0045
0046   Run the example from build directory.
0047
0048   To run the example in batch mode
0049
0050       ./chem3 -mac beam.in
0051
0052   or
0053
0054       ./chem3
0055
0056   then the macro beam.in is processed by default
0057
0058   In interactive mode, run:
0059
0060       ./chem3 -gui
0061
0062   or
0063
0064       ./chem3 -gui gui.mac
0065
0066   The user interface will be launched. Continue using /run/beamOn 1 command.
0067   By default, the vis.mac visualization macro is called.
0068   The vis_vm,.mac macro is used only in the context of the G4DNA tutorial
0069   hands-ons.
0070
0071 ## OUTPUT
0072
0073   Physics initialization and the defined reaction table are printed.
0074   G4ITStepManager processes the chemical stage time step after time step.
0075   Chemical reactions are printed.
0076   In the GUI window a cummulative trajectory of the chemical species is drawn.
0077
0078   The functions in TimeStepAction show how to get species
0079   ID, positions at each time step or in a chemical reaction
0080 ## TIME EVOLUTION VISUALIZATION
0081
0082   User can start a visualization of the chemical track evolution in time and
0083   space using /control/execute movie.mac. (The movie.mac macro then executes
0084   the movie_prep.mac, movie_chemistry.mac and movie_physics.mac macros.)
0085   Note, that in default setup the simulation requires machine with 6 GB of RAM.
0086   To lower memory requirements, either decrease energy of the incident electron
0087   in prep.mac or/and shorten the simulation using SetEndTime setting in
0088   src/ActionInitialization.cc.
0089